Strain identifier

BacDive ID: 18121

Type strain: Yes

Species: Gemella morbillorum

Strain Designation: 2917 B

Strain history: CIP <- 1981, M. Sebald, Inst. Pasteur, Paris, France <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 2917 B

NCBI tax ID(s): 29391 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 8922

BacDive-ID: 18121

DSM-Number: 20572

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Gemella morbillorum 2917 B is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from lung abscess.

NCBI tax id

  • NCBI tax id: 29391
  • Matching level: species

strain history

@refhistory
8922<- ATCC <- L. Holdeman, VPI 5424 <- A. Prévot, 2917 B (Diplococcus morbillorum)
67770DSM 20572 <-- ATCC 27824 <-- L. V. Holdeman VPI 5424 <-- A. R. Prévot 2917B.
121140CIP <- 1981, M. Sebald, Inst. Pasteur, Paris, France <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 2917 B

doi: 10.13145/bacdive18121.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Gemellaceae
  • genus: Gemella
  • species: Gemella morbillorum
  • full scientific name: Gemella morbillorum (Prévot 1933) Kilpper-Bälz and Schleifer 1988
  • synonyms

    @refsynonym
    20215Streptococcus morbillorum
    20215Diplococcus morbillorum
    20215Peptococcus morbillorum

@ref: 8922

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Caryophanales, not assigned to family

genus: Gemella

species: Gemella morbillorum

full scientific name: Gemella morbillorum (Prévot 1933) Kilpper-Bälz and Schleifer 1988

strain designation: 2917 B

type strain: yes

Morphology

cell morphology

  • @ref: 121140
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 121140

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8922PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
38430MEDIUM 38 - for Streptococcus and Gemella HaemolysansyesDistilled water make up to (1000.000 ml);Horse serum (200.000 ml);Glucose (10.000 g);Brain heart infusion agar (52.000 g)
8922COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
121140CIP Medium 253yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=253
121140CIP Medium 38yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=38

culture temp

@refgrowthtypetemperaturerange
8922positivegrowth37mesophilic
38430positivegrowth37mesophilic
67770positivegrowth37mesophilic
121140positivegrowth30-41
121140nogrowth10psychrophilic
121140nogrowth25mesophilic
121140nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8922anaerobe
121140facultative anaerobe

halophily

  • @ref: 121140
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

murein

  • @ref: 8922
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
121140hippurate+hydrolysis606565
121140nitrate-reduction17632
121140nitrite-reduction16301
68380urea-hydrolysis16199
68380arginine-hydrolysis29016
68380D-mannose-fermentation16024
68380raffinose-fermentation16634
68380L-glutamate-degradation29985
68380nitrate-reduction17632
68380tryptophan-energy source27897
68381arginine-hydrolysis29016
68381D-ribose-builds acid from16988
68381D-mannitol-builds acid from16899
68381sorbitol-builds acid from30911
68381lactose-builds acid from17716
68381trehalose-builds acid from27082
68381raffinose-builds acid from16634
68381sucrose+builds acid from17992
68381L-arabinose-builds acid from30849
68381D-arabitol-builds acid from18333
68381alpha-cyclodextrin-builds acid from40585
68381hippurate-hydrolysis606565
68381glycogen-builds acid from28087
68381pullulan-builds acid from27941
68381maltose+builds acid from17306
68381melibiose-builds acid from28053
68381melezitose-builds acid from6731
68381methyl beta-D-glucopyranoside-builds acid from320055
68381D-tagatose-builds acid from16443
68381urea-hydrolysis16199

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6838115688acetoin-
6838035581indole-
12114015688acetoin-

enzymes

@refvalueactivityec
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase-
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase-3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase-3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
121140oxidase-
121140beta-galactosidase-3.2.1.23
121140alcohol dehydrogenase-1.1.1.1
121140catalase-1.11.1.6
121140gamma-glutamyltransferase-2.3.2.2
121140lysine decarboxylase-4.1.1.18
121140ornithine decarboxylase-4.1.1.17
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121140--++-+---+++---+----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
8922----+++---++++-+------+-++++----+------+--+-------
121140----------+/--+/---------+/------+/---+/-----++/---+/---------+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8922------------------++-+/---+++--

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
8922------------+----+-+/------+------
8922------------+----+-+-----+------
8922------------+----+-+-----+------

Isolation, sampling and environmental information

isolation

@refsample type
8922lung abscess
67770Lung abscess
121140Lung abscess

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Lung
#Host Body-Site#Other#Abscess
#Infection#Patient

taxonmaps

  • @ref: 69479
  • File name: preview.99_2849.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_238;96_1510;97_1802;98_2205;99_2849&stattab=map
  • Last taxonomy: Gemella morbillorum subclade
  • 16S sequence: NR_025904
  • Sequence Identity:
  • Total samples: 12902
  • soil counts: 142
  • aquatic counts: 233
  • animal counts: 12420
  • plant counts: 107

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
89222Risk group (German classification)
1211401Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Gemella morbillorum 16S ribosomal RNA sequenceL143271536ena29391
20218Gemella morbillorum strain CCUG 18164 16S-23S ribosomal RNA intergenic spacer, complete sequenceJQ012768205ena29391
8922Gemella morbillorum strain 2917B 16S ribosomal RNA, partial sequenceNR_0259041536nuccore29391
67770Gemella morbillorum gene for 16S ribosomal RNA, partial sequence, strain: JCM 12968LC0962371495ena29391

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Gemella morbillorum NCTC11323GCA_900476045completencbi29391
66792Gemella morbillorum strain FDAARGOS_150129391.35completepatric29391
66792Gemella morbillorum strain NCTC1132329391.4completepatric29391
66792Gemella morbillorum NCTC 113232808606651completeimg29391
66792Gemella morbillorum strain FDAARGOS_150129391.36completepatric29391
66792Gemella morbillorum strain FDAARGOS_150129391.38completepatric29391
66792Gemella morbillorum strain FDAARGOS_150129391.37completepatric29391

GC content

@refGC-contentmethod
892230.0
6777030thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.106no
gram-positiveyes94.16no
anaerobicno69.796yes
aerobicno95.695yes
halophileyes86.557no
spore-formingno90.032no
thermophileno99.637yes
glucose-utilyes83.958no
motileno95.244no
glucose-fermentyes80.114no

External links

@ref: 8922

culture collection no.: DSM 20572, ATCC 27824, JCM 12968, VPI 5424, CCUG 15561, CCUG 18164, CECT 991, CIP 81.10, LMG 18985, NCDO 2228, NCIMB 702228, NCTC 11323

straininfo link

  • @ref: 87109
  • straininfo: 12949

literature

  • topic: Phylogeny
  • Pubmed-ID: 24664577
  • title: Gemella parahaemolysans sp. nov. and Gemella taiwanensis sp. nov., isolated from human clinical specimens.
  • authors: Hung WC, Chen HJ, Tsai JC, Tseng SP, Lee TF, Hsueh PR, Shieh WY, Teng LJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.052795-0
  • year: 2014
  • mesh: Aged, Aged, 80 and over, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Female, Gemella/*classification/genetics/isolation & purification, Genes, Bacterial, Humans, Male, Middle Aged, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan
  • topic2: Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8922Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20572)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20572
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38430Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/11168
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
68382Automatically annotated from API zym
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.https://microbeatlas.org/MicrobeAtlas 1.0 beta
87109Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12949.1StrainInfo: A central database for resolving microbial strain identifiers
121140Curators of the CIPCollection of Institut Pasteur (CIP 81.10)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2081.10